PSG2

pregnancy specific beta-1-glycoprotein 2, the group of V-set domain containing|Pregnancy specific glycoproteins

Basic information

Region (hg38): 19:43064209-43083045

Previous symbols: [ "PSBG2" ]

Links

ENSG00000242221 ∙ NCBI:5670 ∙ OMIM:176391 ∙ HGNC:9519 ∙ Uniprot:P11465 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PSG2 gene.

• not_specified (88 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSG2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000031246.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			84	5		89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	84	5	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSG2	protein_coding	protein_coding	ENST00000406487	5	18835

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.38e-30	4.62e-8	125639	3	78	125720	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.82	353	174	2.03	0.00000972	2130
Missense in Polyphen		102	58.656	1.739		778
Synonymous	-7.33	146	68.7	2.13	0.00000388	682
Loss of Function	-3.98	35	17.2	2.03	0.00000115	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00226	0.00207
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000239	0.000237
Middle Eastern	0.000272	0.000272
South Asian	0.000199	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Intolerance Scores

• loftool: 0.875
• rvis_EVS: 1.4
• rvis_percentile_EVS: 94.75

Haploinsufficiency Scores

• pHI: 0.0777
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0965

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: female pregnancy;cell migration
• Cellular component: cellular_component;extracellular region
• Molecular function: molecular_function